The ability to elucidate RNA structure has broad significance in the study of RNA. Comparative sequence analysis is one method, complementary to experimental procedures, that has yielded important RNA structural information. The sequencing revolution is helping to create larger comparative sequence databases, which in turn creates an opportunity to decipher more RNA structural information. Computationally intensive methods are required to find this information. The purpose of this project, is to develop and refine our correlation analysis, and apply these analysis tools to the question of RNA structure determination. Initial studies are very encouraging, suggesting that continued efforts will result in new structural findings. The results of this analysis have widespread applications, including but no limited to antisense research, overall structural considerations of ribosomal RNAs, and other important RNA molecules, and general RNA structur prediction.